X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fstructure%2FStructureSelectionManager.java;fp=src%2Fjalview%2Fstructure%2FStructureSelectionManager.java;h=34ca6ba50c716ee020778855fb8356a725832d04;hb=a7a69103cb81f7e40803cbed0beb41d05707f641;hp=ad259fd88d0e957830b429597a4c1209cad3f5f2;hpb=3858d4f26e39b36f8bf1d66b22c9d7030fbd6fc0;p=jalview.git

diff --git a/src/jalview/structure/StructureSelectionManager.java b/src/jalview/structure/StructureSelectionManager.java
index ad259fd..34ca6ba 100644
--- a/src/jalview/structure/StructureSelectionManager.java
+++ b/src/jalview/structure/StructureSelectionManager.java
@@ -398,8 +398,9 @@ public class StructureSelectionManager
     {
       // FIXME if sourceType is not null, we've lost data here
       sourceType = AppletFormatAdapter.checkProtocol(pdbFile);
-      pdb = new JmolParser(pdbFile, sourceType);
-
+      pdb = new JmolParser(false, pdbFile, sourceType);
+      pdb.addSettings(parseSecStr, parseSecStr, parseSecStr);
+      pdb.doParse();
       if (pdb.getId() != null && pdb.getId().trim().length() > 0
               && DataSourceType.FILE == sourceType)
       {